Zinc in PDB 3wv1: Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with 4- (2-((6-Fluoro-2-((3-Methoxybenzyl)Carbamoyl)-4-Oxo-3,4- Dihydroquinazolin-5-Yl)Oxy)Ethyl)Benzoic Acid

The structure of Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with 4- (2-((6-Fluoro-2-((3-Methoxybenzyl)Carbamoyl)-4-Oxo-3,4- Dihydroquinazolin-5-Yl)Oxy)Ethyl)Benzoic Acid, PDB code: 3wv1 was solved by H.Oki, Y.Tanaka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.65 / 1.98
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	134.372, 36.058, 95.298, 90.00, 130.90, 90.00
R / Rfree (%)	17.5 / 22

The structure of Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with 4- (2-((6-Fluoro-2-((3-Methoxybenzyl)Carbamoyl)-4-Oxo-3,4- Dihydroquinazolin-5-Yl)Oxy)Ethyl)Benzoic Acid also contains other interesting chemical elements:

Fluorine	(F)	2 atoms
Calcium	(Ca)	4 atoms
Sodium	(Na)	2 atoms

The binding sites of Zinc atom in the Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with 4- (2-((6-Fluoro-2-((3-Methoxybenzyl)Carbamoyl)-4-Oxo-3,4- Dihydroquinazolin-5-Yl)Oxy)Ethyl)Benzoic Acid (pdb code 3wv1). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with 4- (2-((6-Fluoro-2-((3-Methoxybenzyl)Carbamoyl)-4-Oxo-3,4- Dihydroquinazolin-5-Yl)Oxy)Ethyl)Benzoic Acid, PDB code: 3wv1:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with 4- (2-((6-Fluoro-2-((3-Methoxybenzyl)Carbamoyl)-4-Oxo-3,4- Dihydroquinazolin-5-Yl)Oxy)Ethyl)Benzoic Acid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with 4- (2-((6-Fluoro-2-((3-Methoxybenzyl)Carbamoyl)-4-Oxo-3,4- Dihydroquinazolin-5-Yl)Oxy)Ethyl)Benzoic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:17.7 occ:1.00 NE2 A:HIS232 2.1 21.1 1.0 O2 A:FMT306 2.1 22.8 1.0 NE2 A:HIS226 2.1 15.3 1.0 NE2 A:HIS222 2.1 12.7 1.0 O1 A:FMT306 2.4 25.2 1.0 C A:FMT306 2.6 22.5 1.0 CD2 A:HIS232 2.9 21.7 1.0 CD2 A:HIS226 3.1 16.4 1.0 CD2 A:HIS222 3.1 11.7 1.0 CE1 A:HIS232 3.1 21.9 1.0 CE1 A:HIS222 3.1 13.8 1.0 CE1 A:HIS226 3.1 19.2 1.0 O A:HOH715 4.0 32.4 1.0 CG A:HIS232 4.1 16.8 1.0 ND1 A:HIS232 4.1 21.4 1.0 ND1 A:HIS222 4.2 9.7 1.0 CG A:HIS226 4.2 14.8 1.0 ND1 A:HIS226 4.2 12.4 1.0 CG A:HIS222 4.2 13.9 1.0 O A:HOH654 4.4 23.6 1.0 OE2 A:GLU223 4.4 18.6 1.0 O34 A:WHH307 4.5 15.4 1.0 CE A:MET240 4.7 10.0 1.0 C35 A:WHH307 4.9 16.4 1.0 OE1 A:GLU223 4.9 19.4 1.0 O A:HOH651 5.0 41.2 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with 4- (2-((6-Fluoro-2-((3-Methoxybenzyl)Carbamoyl)-4-Oxo-3,4- Dihydroquinazolin-5-Yl)Oxy)Ethyl)Benzoic Acid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with 4- (2-((6-Fluoro-2-((3-Methoxybenzyl)Carbamoyl)-4-Oxo-3,4- Dihydroquinazolin-5-Yl)Oxy)Ethyl)Benzoic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:17.7 occ:1.00 OD2 A:ASP174 1.9 23.5 1.0 NE2 A:HIS172 2.0 20.1 1.0 NE2 A:HIS187 2.0 16.0 1.0 ND1 A:HIS200 2.1 15.9 1.0 CD2 A:HIS172 2.8 19.1 1.0 CE1 A:HIS187 2.8 19.6 1.0 CG A:ASP174 2.8 22.0 1.0 CE1 A:HIS172 3.1 22.7 1.0 CE1 A:HIS200 3.1 23.0 1.0 CG A:HIS200 3.1 18.7 1.0 OD1 A:ASP174 3.1 18.0 1.0 CD2 A:HIS187 3.1 18.4 1.0 CB A:HIS200 3.4 15.9 1.0 ND1 A:HIS187 4.0 21.6 1.0 CG A:HIS172 4.0 16.6 1.0 ND1 A:HIS172 4.1 21.7 1.0 O A:TYR176 4.1 24.3 1.0 NE2 A:HIS200 4.2 18.3 1.0 CG A:HIS187 4.2 12.3 1.0 CD2 A:HIS200 4.2 18.4 1.0 CB A:ASP174 4.2 23.8 1.0 CE1 A:PHE189 4.4 25.7 1.0 CE2 A:PHE178 4.7 12.2 1.0 CZ A:PHE178 4.7 10.3 1.0 CB A:TYR176 4.7 24.2 1.0 CZ A:PHE189 4.8 26.6 1.0 O A:HOH620 4.9 16.0 1.0 CA A:HIS200 4.9 15.7 1.0 C A:TYR176 5.0 25.4 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with 4- (2-((6-Fluoro-2-((3-Methoxybenzyl)Carbamoyl)-4-Oxo-3,4- Dihydroquinazolin-5-Yl)Oxy)Ethyl)Benzoic Acid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with 4- (2-((6-Fluoro-2-((3-Methoxybenzyl)Carbamoyl)-4-Oxo-3,4- Dihydroquinazolin-5-Yl)Oxy)Ethyl)Benzoic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:30.5 occ:1.00 NE2 B:HIS226 2.1 22.5 1.0 NE2 B:HIS222 2.1 29.5 1.0 NE2 B:HIS232 2.2 41.4 1.0 O2 B:FMT306 2.2 43.3 1.0 O1 B:FMT306 2.5 44.6 1.0 C B:FMT306 2.7 45.0 1.0 CE1 B:HIS232 3.0 43.2 1.0 CE1 B:HIS226 3.0 24.6 1.0 CD2 B:HIS222 3.0 22.8 1.0 CD2 B:HIS232 3.1 37.3 1.0 CD2 B:HIS226 3.1 25.2 1.0 CE1 B:HIS222 3.2 24.4 1.0 ND1 B:HIS232 4.0 40.4 1.0 CG B:HIS232 4.1 35.6 1.0 ND1 B:HIS226 4.2 29.7 1.0 CG B:HIS222 4.2 26.3 1.0 CG B:HIS226 4.2 23.7 1.0 ND1 B:HIS222 4.3 27.4 1.0 O B:HOH635 4.4 35.4 1.0 CE B:MET240 4.6 25.4 1.0 OE2 B:GLU223 4.6 26.5 1.0 OE1 B:GLU223 4.8 25.9 1.0 O B:HOH664 4.9 47.1 1.0 CD B:GLU223 5.0 25.5 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with 4- (2-((6-Fluoro-2-((3-Methoxybenzyl)Carbamoyl)-4-Oxo-3,4- Dihydroquinazolin-5-Yl)Oxy)Ethyl)Benzoic Acid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with 4- (2-((6-Fluoro-2-((3-Methoxybenzyl)Carbamoyl)-4-Oxo-3,4- Dihydroquinazolin-5-Yl)Oxy)Ethyl)Benzoic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:23.9 occ:1.00 OD2 B:ASP174 1.8 22.2 1.0 NE2 B:HIS172 1.9 23.5 1.0 NE2 B:HIS187 2.0 22.3 1.0 ND1 B:HIS200 2.0 22.8 1.0 CG B:ASP174 2.8 24.6 1.0 CD2 B:HIS172 2.9 19.9 1.0 CE1 B:HIS187 2.9 16.3 1.0 CE1 B:HIS172 3.0 23.3 1.0 CE1 B:HIS200 3.0 19.7 1.0 CG B:HIS200 3.0 18.9 1.0 CD2 B:HIS187 3.0 20.9 1.0 OD1 B:ASP174 3.2 24.3 1.0 CB B:HIS200 3.4 20.2 1.0 ND1 B:HIS187 4.0 21.3 1.0 CG B:HIS172 4.0 19.9 1.0 ND1 B:HIS172 4.1 20.9 1.0 CG B:HIS187 4.1 23.2 1.0 NE2 B:HIS200 4.1 20.2 1.0 CB B:ASP174 4.1 21.3 1.0 CD2 B:HIS200 4.2 24.5 1.0 O B:TYR176 4.2 22.3 1.0 CZ B:PHE178 4.6 23.6 1.0 CE2 B:PHE178 4.6 21.9 1.0 CE1 B:PHE189 4.7 28.9 1.0 CZ B:PHE189 4.8 28.6 1.0 O B:HOH605 4.8 23.0 1.0 CA B:HIS200 4.8 20.0 1.0 CB B:TYR176 4.8 27.5 1.0

H.Nara, K.Sato, T.Naito, H.Mototani, H.Oki, Y.Yamamoto, H.Kuno, T.Santou, N.Kanzaki, J.Terauchi, O.Uchikawa, M.Kori. Discovery of Novel, Highly Potent, and Selective Quinazoline-2-Carboxamide-Based Matrix Metalloproteinase (Mmp)-13 Inhibitors Without A Zinc Binding Group Using A Structure-Based Design Approach J.Med.Chem. V. 57 8886 2014.
ISSN: ISSN 0022-2623
PubMed: 25264600
DOI: 10.1021/JM500981K